This prototype was on sale on Yahoo Japan auctions back in July 2009, along with a prototype of Gokujou Parodius. The date on the label is October 24, 1994, which is about two months before the commercial release. This is just a sample cart and as such, it is pretty close to the final version. Matthew Callis released this a while back on his site eludevisibility.org, but for whatever reason, it doesn't appear that the ROM image was widely distributed.

Not really a visible difference, but the cut screens in the prototype go a bit faster.

prototype

final

In the final version, the place on the screen where Goemon is centered is higher up. As a result, you can see further to the bottom of the screen.

prototype

final

There are a few differences in the text of the game.

prototype

final

prototype

final

A pretty minor thing, the placement of Goemon when he enters buildings is slightly different in the prototype.

prototype

final

Goemon walks faster in the prototype.

prototype - left; final - right

Pressing the "R" button enables a "walk through walls" mode. Float anywhere you want without any consequence!

prototype

Well, not exactly. I got to this shrine that is otherwise inaccessible, and it causes the game to either reset or crash.

prototype

I also noticed that if you run out of money, the money counter goes to 9999.

Seeing as how this is a sample cart, the programmers placed a limit on how far you could go. Once you get to this spot, you cannot enter the room to the right, and therefore you cannot proceed further into the game. The side-by-side comparison between the prototype and final version of this level up to this point was identical.